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DNA Microarray Quality Control Carlo Colantuoni ccolantu@jhsph April 25, 2007

DNA Microarray Quality Control Carlo Colantuoni ccolantu@jhsph.edu April 25, 2007. OR …. How many different ways can we look at global expression data?. Microarray Quality Control Depends on Technology. NHGRI Microarray Core Facility - Abdel Elkalhoun

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DNA Microarray Quality Control Carlo Colantuoni ccolantu@jhsph April 25, 2007

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  1. DNA Microarray Quality Control Carlo Colantuoni ccolantu@jhsph.edu April 25, 2007

  2. OR …

  3. How many different ways can we look at global expression data?

  4. Microarray Quality Control Depends on Technology

  5. NHGRI Microarray Core Facility - Abdel Elkalhoun Oligonucleotide : 2-color Glass : Fluorescence : 36K

  6. Illumina Microarray Platform Oligonucleotides : Beads : 24K : High Redundancy

  7. NIA cDNA microarray Core Facility Nylon P33 9600 MGC elements

  8. Affymetrix - short oligos : many 10,000’s

  9. Outlier Identification in Microarray Quality Control

  10. Microarray Pseudo Images: Intensity

  11. Microarray Pseudo Images: Ratios

  12. Images of probe level data This is the raw data

  13. Images of probe level data Residuals (or weights) from probe level model fits show problem clearly

  14. Artifact & Bias Removal in Microarray Quality Control

  15. Intensities and Ratios Red Log Ratio Green Intensity

  16. 4 arrays: Raw Log Intensities

  17. 4 arrays: Raw Linear Intensities

  18. 1 array: Ratio v. Intensity

  19. Print-tip Effect

  20. Bad Plate Effect

  21. Bad Plate Effect

  22. Print Order Effect

  23. Uncorrected Intensities: MDS Colored by Batch

  24. Much Like Red:Green Analysis Removing The Batch Effect

  25. Uncorrected Intensities: MDS Colored by Batch

  26. Batch Subtracted Measures: MDS Colored by Batch

  27. MDS of All Array Experiments: Subject Replicates

  28. Hybridization Artifacts

  29. AGE ?

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